question

activation domain does what

answer

recruits the transcription machinery

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basic region/leucine zipper (bzip) protein

answer

is usually found as part of a DNA binding domain in various transcription factors, and are therefore involved in regulating gene expression. Functions as a dimerizaiton domain. Its presence generates adhesion forces in parallel alpha helices.

question

bzip DNA binding domain

answer

One part of the domain contains a region that mediates sequence specific DNA properties and the leucine zipper that is required for the dimerization of two DNA binding regions.

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CCAAT box

answer

is a distinct pattern of nucleotides with GGCCAATCT consensus sequence that occure upstream by 75-80 bases to the initial transcription site. It signals the binding site for the RNA transcription factor -located upstream from the TATA box (in eukaryotes)

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chromatin remodeling

answer

is the enzyme assisted movement of nucleosomes on DNA. At the core of a chromatin remodeling complexes is an ATPase capable of DNA translocation. By moving nucleosomes, transcription factors can get access to DNA that was unavailable.

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Dimerization domain

answer

question

DNA affinity chromatography

answer

a method of separating biochemical mixtures and based on a highly specific biological interaction such as that between antigen and antibody, enzyme and substrate, or receptor and ligand.

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DNA binding domain

answer

question

enhancer

answer

s a short region of DNA that can be bound with proteins (trans-acting factors much like transcription factors) to enhance transcription levels of genes. Enhancers are usually cis acting but it does not need to be particularly close to the genes it acts on., and sometimes not even on the same chromosome. It is typically close to the promoter and the gene.

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euchromatin

answer

is a lightly packed form of chromatin that is rich in gene concentration and is often, but not always, under active transcription. Is the most active portion of the genome within the cell nucleus.

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GAL4

answer

is a biochemical method used to study gene expression and function in organisms such as the fruit fly. Has two parts, the GAL4 gene, which encodes the yeast transcription activator protein Gal4 and the UAS (upstream activation sequence) a short section of the promoter region to which Gal4 specifically binds to activate gene transcription.

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gene splicing

answer

Is the process of combining two or more sequences that would not normally occur together

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helix-loop-helix motif

answer

is characterized by two a-helicies connected by a loop. The larger helix typically contains the DNA binding regions.

question

heterochromatin

answer

is a tightly packed form of DNA which comes in different varieties. These varieties lie on a constitutive and facultative.

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histone acetylase (HAT)

answer

are enzymes that acetylate conserved lysine amino acids on histone proteins by transferring an acetyl group from acetyl CoA to fomr E-N-acetyl lysine. In general it is linked to transcriptional activation and associated with euchromatin.

question

histone deacetylase (HDAC)

answer

are a class of enzymes that remove acetyl groups from an E-N-acetyl lysine amino acid on a histone. It is opposite that of HAT

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homeobox

answer

is a DNA sequence found within genes that are involved in the regulation of patterns of anatomical development in animals, fungi, and plants. It is about 180 base pairs long and encodes a protein domain (homeodomain) which when expressed can bind DNA.

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homeodomain

answer

is a protein structural domain that binds DNA or RNA and is thus commonly found in transcription factors. Has three alpha helicies and it is the third helix that interacts directly with DNA.

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homeotic gene

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are genes that determine which parts of the body form what what body parts.

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hormone response element

answer

is a short sequence of DNA within the promoter of a a gene that is able to bind a specific hormone receptor complex and therefore regulate transcription. The sequence is most commonly a pair of inverted repeats separated by three nucleotides which also indicates that the receptor binds as a dimer.

question

leucine zipper

answer

is a motif that is involved as part of a DNA binding domain in various transcription factors, and are therefore involved in regulating gene expression. It involves parallel alpha helices, with a hydrophobic region running along one side.

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ligand binding domain

answer

Ligand binding to a receptor alters the chemical conformation (3-D shape). This affects the functional state of the a receptor.

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linker-scanning mutagenesis

answer

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nuclear receptor

answer

are a class of proteins found within cells that are responsible for sensing steroid and thyroid hormones and certain other molecules. These work with other proteins to regulate the expression of specific genes, thereby controlling development, homeostasis, and metabolism of the organism.

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POU domain

answer

(POU comes from the three transcription factors that are used) are eukaryotic transcription factors containing a bipartite DNA binding domain

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POU protein

answer

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remodeling complex

answer

is a complex with the capacity to remodel the structure of chromatin. It exhibits a DNA dependent ATPase activity stimulated by both free and nucleosomeal DNA and a capacity to perturb nucleosome structures.

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transcription activator protein do what?

answer

they help recruit the transcription machinery

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two hybrid assay

answer

this utilizes a genetically engineered strain of yeast in which the biosynthesis of certain nutrients (usually amino acids or nucleic acids) is lacking. When grown on a media that lacks these nutrients, the yeast dies. This mutant yeast strain can be made to incorporate foreign DNA in the form of plasmids

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upstream activating sequence (UAS)

answer

is a cis-acting regulatory sequence. It is distinct from the promoter and increases the expression of a neighboring gene. Its binds GAL4

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zinc finger

answer

is a protein structural motif that can coordinate one or more zinc ions to help stabilize their folds. They function as interaction modules that bind DNA, RNA, proteins, or small molecules.

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What are the types of DNA binding domains?

answer

Zinc fingers, helix-turn-helix structures, basic region/ leucine zipper proteins and helix-loop-helix motifs.

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What has been a key technique in identifying promoter elements

answer

Linker scanning mutagenesis

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What binds just upstream of the core promoter elements to bind specific transcription activator protein?

answer

Promoter proximal elements

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Enhancers do what?

answer

They modulate transcription and can act at a great distance from the promoter.

question

The DNA binding domain of transcription activators make sequence specific contacts with ____ or ______?

answer

Enhancers or promoter proximal elements

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The _____ ______ recruits the transcription machinery

answer

activation domain

question

Nuclear localization and nuclear export signals do what?

answer

They permit activator proteins to move into or out of the nucleus.

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What can be used to purify activator proteins?

answer

DNA affinity chromatography.

question

Homeotic genes do what

answer

they encode important transcriptional activators called homeobox proteins that help define the body axes during development.

question

The homeodomain of a homeobox protein contains what?

answer

a helix-turn-helix motif for DNA binding.

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POU proteins have what

answer

Both a homeobox and a POU domain for DNA binding.

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What is the classical zinc finger model

answer

Cys2His2- zinc residues are bound by two Cys and two His residues

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Nuclear receptors have ____ ____ motifs. The nuclear receptors have a common structural design and are _____ or _____ with a recognition helix that bind to a hormone response element.

answer

Zinc Finger, homodimers or heterodimers.

question

_____ proteins bind to DNA as dimers that are held together through coiled coil interactions.

answer

Bzip

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Where do activator proteins with a helix-loop-helix motif bind as dimers?

answer

To the major groove of DNA

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In an activator, what must be bound to a DNA binding domain to stimulate transcription?

answer

The activation domain

question

How do activators work

answer

They can work through recruitment of the transcriptional machinery or by inducing a conformational change in the transcriptional machinery.

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What is one of the best studied transcriptional activators? What has it shown?

answer

Gal4- It has been shown that the activation domain cannot stimulate transcription without a DNA binding domain.

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Chromatin remodeling factors do what

answer

They alter histone-DNA or histone-histone interactions to make DNA accessible to the transcription machinery. These complexes work without producing covalent modification in chromatin.

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Modifying complexes does what?

answer

it modifies the histone tails to activate or repress transcription.

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What tends to activate transcription? What tends to repress transcription?

answer

Acetylation by HATs, Histone deacetylation by HDACs.

question

Chromatin remodeling and chromatin modifying complexes interact how?

answer

They interact with each other and with the transcription machinery to condense or decondense DNA to silence genes or make genes transcriptionally active

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Enhancers differ from other regulatory sequences in what way?

answer

They act at a distance

question

Each transcription activator protein has at least two independently folding domains: an activation domain and what

answer

DNA binding domain

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Genes that assign positional identities to cells along the anterior posterior axis of an embryo are called ____ genes

answer

homeotic

question

The helix turn helix motif or homeodomain is required for ____

answer

DNA binding

question

In a classical zinc finger, zinc ions...

answer

interact with histidine and methionine residues

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Members of the nuclear receptor superfamily are induced to activate transcription by___?

answer

ligand binding

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One reason that the number of nuclear receptors is greater than the total number of genes encoding nuclear receptors is that____?

answer

The proteins form heterodimers

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Leucine zippers are characterized by ___

answer

coiled coil interactions

question

Leucine zippers have ____ DNA binding domains?

answer

fibrous

question

What does the b stand for in bZip of bHLH?

answer

basic

question

Myc, Max, and Mad are transcription factors of the ___ family.

answer

HLHbzip

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Transcription will be stimulated as long as the DNA-binding domain and activation domain____.

answer

are both present, either covalently or noncovalently linked

question

What are two possible ways an activator protein can affect transcription?

answer

1. recruits transcriptional machinery
2. induces a conformational change in the transcriptional apparatus that stimulates transcription initiation.

question

Euchromatin, which contains many _____, is usually ____ accessible to transcription machinery

answer

protein coding genes; more

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Histone deacetlyation lowers transcriptional activity by _____

answer

stabilizing compact chromatin structure

question

What are known post-translational histone modifications

answer

1. Serine phosphorylation
2. lysine methylation
3. lysine ubiquitination

question

A DNA that serves as a binding site for proteins that create a repressive chromatin environment is called a

answer

silencer

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